BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524369.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 2,803,777
number of mapped reads = 2,576,694 (91.9%)
number of supplementary alignments = 13,115 (0.47%)
number of secondary alignments = 0
number of mapped bases = 151,998,516 bp
number of sequenced bases = 151,954,560 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 207,771
duplication rate = 5.92%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3294
>>>>>>> ACTG content
number of A's = 37,411,604 bp (24.62%)
number of C's = 30,419,107 bp (20.02%)
number of T's = 46,911,834 bp (30.87%)
number of G's = 37,190,625 bp (24.47%)
number of N's = 21,390 bp (0.01%)
GC percentage = 44.49%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 787,488
number of insertions = 12,542
mapped reads with insertion percentage = 0.48%
number of deletions = 27,546
mapped reads with deletion percentage = 1.06%
homopolymer indels = 39.78%
>>>>>>> Coverage
mean coverageData = 0.0491X
std coverageData = 0.4737X
There is a 3.94% of reference with a coverageData >= 1X
There is a 0.66% of reference with a coverageData >= 2X
There is a 0.14% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 12468172 0.050022631638699105 0.9300014708234527
chr2 243199373 12238434 0.05032263796173521 0.6258631035314568
chr3 198022430 10039037 0.0506964640318776 0.26998556790072703
chr4 191154276 9438930 0.04937859721223291 0.3545479391568317
chr5 180915260 9162452 0.05064499257829329 0.2742974869362811
chr6 171115067 8524232 0.049815788576934604 0.3003523151407105
chr7 159138663 8530592 0.05360477359295145 0.5810630349031288
chr8 146364022 7841908 0.053578112249470705 0.43286982331872814
chr9 141213431 6449254 0.04567025922626298 0.36884116997400396
chr10 135534747 7348576 0.05421912950484941 0.4712805724355788
chr11 135006516 6820295 0.050518265355429214 0.3937484440801514
chr12 133851895 6712468 0.05014847193609026 0.2769678500489107
chr13 115169878 4529037 0.03932483978145744 0.23993777252775017
chr14 107349540 4523440 0.04213748843264722 0.2688820576605243
chr15 102531392 4326953 0.0422012509105504 0.2462169977817448
chr16 90354753 4619139 0.051122258062063435 0.30346772241364356
chr17 81195210 4359886 0.053696344895222264 0.3153167590816659
chr18 78077248 3983225 0.05101646256794297 0.7822924093848335
chr19 59128983 3326860 0.05626445494589345 0.6045242202167127
chr20 63025520 3358756 0.05329199981213959 0.2919333580552052
chr21 48129895 2027931 0.042134540289356544 0.3262162938814507
chr22 51304566 1977076 0.038536063242402246 0.24068991364423786
chrMT 16571 408385 24.64455977309758 14.975278924813512
chrX 155270560 8445528 0.05439233297026816 0.3223581943979072
chrY 59373566 537950 0.009060429349990533 0.2808712489982976